First commit

.gitignore

+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+

.gitlab-ci.yml

+image: gradle:jdk16
+
+before_script:
+  - export GRADLE_USER_HOME=`pwd`/.gradle
+
+cache:
+  paths:
+    - .gradle/wrapper
+    - .gradle/caches
+
+java:
+  stage: test
+  script:
+    - gradle test
+  artifacts:
+    when: always
+    reports:
+      junit: build/test-results/test/**/TEST-*.xml
\ No newline at end of file

README.md

+# Réseau de régulation de gènes
+
+## Description du projet
+
+Dans cette planche de TP, vous allez implémenter des classes pour simuler un réseau régulation de gènes.
+
+## Membre du projet
+
+- NOM, prénom
\ No newline at end of file

build.gradle

+plugins {
+    id 'application'
+    id "org.openjfx.javafxplugin" version "0.0.13"
+}
+
+javafx {
+    version = "19"
+    modules = [ 'javafx.controls', 'javafx.fxml' ]
+}
+
+repositories {
+    mavenCentral()
+}
+
+dependencies {
+    testImplementation('org.junit.jupiter:junit-jupiter-api:5.9.0',
+            'org.assertj:assertj-core:3.23.1')
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.9.0'
+}
+
+test {
+    useJUnitPlatform()
+}
+
+application {
+    mainClassName = "viewer.MainApp"
+}
\ No newline at end of file

gradle/wrapper/gradle-wrapper.properties

+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
\ No newline at end of file

gradlew

+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
+done
+
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='-Dfile.encoding=UTF-8 "-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+    echo "$*"
+} >&2
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD=$JAVA_HOME/jre/sh/java
+    else
+        JAVACMD=$JAVA_HOME/bin/java
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD=java
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
+        fi
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
+    done
+fi
+
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
+
+exec "$JAVACMD" "$@"

gradlew.bat

+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

settings.gradle

+rootProject.name = 'regulatory-network'
+

src/main/java/model/events/SimulationEvent.java

+package model.events;
+
+import model.genes.RegulatoryGene;
+
+import java.util.List;
+
+public interface SimulationEvent extends Comparable<SimulationEvent> {
+  void updateGenes();
+  double getTime();
+
+  List<RegulatoryGene> getGenes();
+
+  String getInfo();
+
+}

src/main/java/model/genes/ConstantRegulatoryGene.java

+package model.genes;
+
+import model.regulators.Regulator;
+
+public class ConstantRegulatoryGene implements RegulatoryGene{
+  private double proteinConcentration;
+  private final double initialProteinConcentration;
+  private final String name;
+  private boolean isSignaled;
+
+  public ConstantRegulatoryGene(String name, double proteinConcentration, boolean isSignaled) {
+    this.proteinConcentration = proteinConcentration;
+    this.initialProteinConcentration = proteinConcentration;
+    this.name = name;
+    this.isSignaled = isSignaled;
+  }
+
+  @Override
+  public Regulator getRegulator() {
+    return null;
+  }
+
+  @Override
+  public double getInitialProteinConcentration() {
+    return initialProteinConcentration;
+  }
+
+  @Override
+  public double getProteinConcentration() {
+    return proteinConcentration;
+  }
+
+  @Override
+  public void setProteinConcentration(double proteinConcentration) {
+    this.proteinConcentration = proteinConcentration;
+  }
+
+  @Override
+  public String toString() {
+    return name;
+  }
+
+  @Override
+  public void update() {
+
+  }
+
+  @Override
+  public void setRegulator(Regulator regulator) {
+
+  }
+
+  @Override
+  public boolean isSignaled() {
+    return isSignaled;
+  }
+
+  @Override
+  public void setSignaled(boolean isSignaled) {
+    this.isSignaled = isSignaled;
+  }
+}

src/main/java/model/genes/Gene.java

+package model.genes;
+
+public interface Gene {
+  double getProteinConcentration();
+  double getInitialProteinConcentration();
+  void setProteinConcentration(double proteinConcentration);
+  String toString();
+  void update();
+}

src/main/java/model/genes/RegulatoryGene.java

+package model.genes;
+
+import model.regulators.Regulator;
+
+public interface RegulatoryGene extends Gene{
+  Regulator getRegulator();
+  void setRegulator(Regulator regulator);
+  boolean isSignaled();
+  void setSignaled(boolean isSignaled);
+}

src/main/java/model/network/RegulatoryNetwork.java

+package model.network;
+
+import javafx.scene.chart.XYChart;
+import model.events.SimulationEvent;
+import model.genes.RegulatoryGene;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class RegulatoryNetwork {
+  private final List<RegulatoryGene> genes;
+  private final double timeStepLength;
+  private final double timeUpperBound;
+  private List<XYChart.Series<Number, Number>> seriesList;
+
+  public List<RegulatoryGene> getGenes() {
+    return genes;
+  }
+
+  public List<SimulationEvent> getSimulationEvents() {
+    return simulationEvents;
+  }
+
+  public double getTimeStepLength() {
+    return timeStepLength;
+  }
+
+  public double getTimeUpperBound() {
+    return timeUpperBound;
+  }
+
+  private final List<SimulationEvent> simulationEvents = new ArrayList<>();
+
+  public RegulatoryNetwork(List<RegulatoryGene> genes, List<SimulationEvent> simulationEvents, double timeStepLength, double timeUpperBound) {
+    this.genes = genes;
+    this.timeStepLength = timeStepLength;
+    this.timeUpperBound = timeUpperBound;
+    this.simulationEvents.addAll(simulationEvents);
+    Collections.sort(simulationEvents);
+  }
+
+  public List<XYChart.Series<Number, Number>> getData() {
+    initializeSeriesList();
+    simulateGenes();
+    return seriesList;
+  }
+
+  private void simulateGenes() {
+    for(int stepCount = 0; stepCount * timeStepLength <= timeUpperBound; stepCount++){
+      double time = stepCount * timeStepLength;
+      manageEvents(time);
+      collectData(time);
+      updateGenes();
+    }
+  }
+
+  private void manageEvents(double time) {
+    List<SimulationEvent> currentEvents = getCurrentEvents(time);
+    applyToGenes(currentEvents);
+  }
+
+  private void applyToGenes(List<SimulationEvent> currentEvents) {
+    for(SimulationEvent event : currentEvents)
+      event.updateGenes();
+  }
+
+  private List<SimulationEvent> getCurrentEvents(double time) {
+    List<SimulationEvent> currentEvents = new ArrayList<>();
+    for(SimulationEvent event : simulationEvents) {
+      if (event.getTime() == time) {
+        currentEvents.add(event);
+      }
+    }
+    return currentEvents;
+  }
+
+  private void updateGenes() {
+    for (RegulatoryGene gene : genes) {
+      gene.update();
+    }
+  }
+
+  private void collectData(double time) {
+    for(int index = 0; index < genes.size(); index++) {
+      seriesList.get(index).getData().add(new XYChart.Data<>(time, genes.get(index).getProteinConcentration()));
+    }
+  }
+
+
+  private void initializeSeriesList() {
+    seriesList = new ArrayList<>();
+
+    for (RegulatoryGene gene : genes) {
+      XYChart.Series<Number, Number> series = new XYChart.Series<>();
+      series.setName(gene.toString());
+      seriesList.add(series);
+    }
+  }
+
+}

src/main/java/model/network/RegulatoryNetworkDataManager.java

+package model.network;
+
+import model.events.SimulationEvent;
+import model.genes.ConstantRegulatoryGene;
+import model.genes.RegulatoryGene;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class RegulatoryNetworkDataManager {
+  public void write(BufferedWriter bufferedWriter, RegulatoryNetwork regulatoryNetwork) throws IOException {
+    bufferedWriter.write("TimeStep " + regulatoryNetwork.getTimeStepLength() + "\n");
+    bufferedWriter.write("TimeUpperBound " + regulatoryNetwork.getTimeUpperBound() + "\n");
+    writeGenes(bufferedWriter, regulatoryNetwork);
+    writeEvents(bufferedWriter, regulatoryNetwork);
+  }
+
+  private static void writeEvents(BufferedWriter bufferedWriter, RegulatoryNetwork regulatoryNetwork) throws IOException {
+    for(SimulationEvent event : regulatoryNetwork.getSimulationEvents()){
+      StringBuilder eventString = new StringBuilder(event.getClass().getSimpleName() + " ");
+      eventString.append(event.getTime()).append(" ");
+      List<RegulatoryGene> genes = event.getGenes();
+      for(int index = 0; index < genes.size(); index++){
+        if(index!=0) {
+          eventString.append(",");
+        }
+        eventString.append(genes.get(index));
+      }
+      eventString.append(" ");
+      eventString.append(event.getInfo()).append("\n");
+      bufferedWriter.write(eventString.toString());
+    }
+  }
+
+  private static void writeGenes(BufferedWriter bufferedWriter, RegulatoryNetwork regulatoryNetwork) throws IOException {
+    for(RegulatoryGene gene : regulatoryNetwork.getGenes()){
+      String geneString = gene.getClass().getSimpleName() + " ";
+      geneString += gene + " ";
+      geneString += gene.getInitialProteinConcentration() + " ";
+      geneString += gene.isSignaled() + "\n";
+      bufferedWriter.write(geneString);
+    }
+  }
+
+  public RegulatoryNetwork read(BufferedReader bufferedReader) throws IOException {
+    Map<String,RegulatoryGene> genes = new HashMap<>();
+    List<SimulationEvent> events = new ArrayList<>();
+
+    double timeUpperBound = 20;
+    double timeStepLength = 0.01;
+
+    int lineNumber = 0;
+
+    for (String line = bufferedReader.readLine(); line != null; line = bufferedReader.readLine()){
+      String[] tokens = line.split(" ");
+      switch (tokens[0]){
+        case "TimeStep" -> timeStepLength = Double.parseDouble(tokens[1]);
+        case "TimeUpperBound" -> timeUpperBound = Double.parseDouble(tokens[1]);
+        case "ConstantRegulatoryGene" -> readConstantRegulatoryGene(genes, tokens);
+        default -> throw new IOException("Parse error line " + lineNumber);
+      }
+      lineNumber++;
+    }
+    return new RegulatoryNetwork(new ArrayList<>(genes.values()), events, timeStepLength, timeUpperBound);
+  }
+
+  private static void readConstantRegulatoryGene(Map<String, RegulatoryGene> genes, String[] tokens) {
+    String name = tokens[1];
+    double concentration = Double.parseDouble(tokens[2]);
+    boolean isSignaled = Boolean.parseBoolean(tokens[3]);
+    genes.put(name, new ConstantRegulatoryGene(name, concentration, isSignaled));
+  }
+
+  public RegulatoryNetwork generate() {
+    List<RegulatoryGene> genes = new ArrayList<>();
+    RegulatoryGene x = new ConstantRegulatoryGene("X", 3, true);
+    genes.add(x);
+    RegulatoryGene y = new ConstantRegulatoryGene("Y", 2, true);
+    genes.add(y);
+    RegulatoryGene z = new ConstantRegulatoryGene("Z", 4, false);
+    genes.add(z);
+    List<SimulationEvent> simulationEvents = new ArrayList<>();
+    return new RegulatoryNetwork(genes, simulationEvents, 0.01, 20);
+  }
+
+
+}

src/main/java/model/regulators/Regulator.java

+package model.regulators;
+
+public interface Regulator {
+  double inputFunction();
+}

src/main/java/viewer/GeneChart.java

+package viewer;
+
+import javafx.geometry.Side;
+import javafx.scene.chart.LineChart;
+import javafx.scene.chart.NumberAxis;
+
+
+import java.util.List;
+
+public class GeneChart extends LineChart<Number, Number> {
+  private static final double X_TICK_UNIT = 1;
+  private static final double X_LOWER_BOUND = 0;
+  private static final double Y_LOWER_BOUND = 0;
+  private static final double Y_TICK_UNIT = 1;
+  public static final int X_UPPER_BOUND = 20;
+  public static final int Y_UPPER_BOUND = 10;
+
+
+  public GeneChart(){
+    super(new NumberAxis(X_LOWER_BOUND, X_UPPER_BOUND, X_TICK_UNIT),
+            new NumberAxis(Y_LOWER_BOUND, Y_UPPER_BOUND, Y_TICK_UNIT));
+    getXAxis().setSide(Side.BOTTOM);
+    getYAxis().setSide(Side.LEFT);
+    setCreateSymbols(false);
+    getYAxis().setAutoRanging(true);
+  }
+
+  public void plot(List<Series<Number, Number>> seriesList, double timeUpperBound){
+    ((NumberAxis) getXAxis()).setUpperBound(timeUpperBound);
+    getData().clear();
+    for(Series<Number, Number> series : seriesList){
+      getData().add(series);
+    }
+  }
+}

src/main/java/viewer/MainApp.java

+package viewer;
+
+import javafx.application.Application;
+import javafx.fxml.FXMLLoader;
+import javafx.scene.Parent;
+import javafx.scene.Scene;
+import javafx.scene.layout.AnchorPane;
+import javafx.scene.layout.BorderPane;
+import javafx.stage.Stage;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Objects;
+
+public class MainApp extends Application {
+
+  private Stage primaryStage;
+  private AnchorPane rootLayout;
+  public static void main(String[] args) {
+    Application.launch(MainApp.class, args);
+  }
+
+  @Override
+  public void start(Stage stage) {
+    this.primaryStage = stage;
+    this.primaryStage.setTitle("Regulatory Network");
+    initRootLayout();
+  }
+
+  public void initRootLayout() {
+    try {
+      // Load root layout from fxml file.
+      FXMLLoader loader = new FXMLLoader(getClass().getResource("/MainApp.fxml"));
+      rootLayout = loader.load();
+
+      // Show the scene containing the root layout.
+      Scene scene = new Scene(rootLayout);
+      primaryStage.setScene(scene);
+
+      // Give the controller access to the main app.
+      MainAppController controller = loader.getController();
+      controller.setMainApp(this);
+
+      primaryStage.show();
+    } catch (IOException e) {
+      e.printStackTrace();
+    }
+
+  }
+
+  public Stage getPrimaryStage() {
+    return primaryStage;
+  }
+
+}